Bioinformatics analysis of microRNA comprehensive regulatory network in congenital microtia

Genetics and Epigenetics in the Genesis and Development of Microtia

Microtia is a congenital malformation of the external and middle ear associated with varying degrees of severity that range from mild structural abnormalities to the absence of the external ear and auditory canal. Globally, it is the second most common congenital craniofacial malformation and is typically caused by inherited defects, external factors, or the interaction between genes and external factors. Epigenetics notably represents a bridge between genetics and the environment. This review has devoted attention to the current proceedings of the genetics and epigenetics of microtia and related syndromes.

Profiling of Long Non-Coding RNAs in Auricular Cartilage of Patients with Isolated Microtia

Introduction: Microtia is the second most common maxillofacial birth defect worldwide. However, the involvement of long non-coding RNAs (lncRNAs) in isolated microtia is not well understood. This study aimed at identifying lncRNAs that regulate the expression of genes associated with isolated microtia. Methods: We used our microarray data to analyze the expression pattern of lncRNA in the auricular cartilage tissues from 10 patients diagnosed with isolated microtia, alongside 15 control subjects. Five lncRNAs were chosen for validation using real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Results: We identified 4651 differentially expressed lncRNAs in the auricular cartilage from patients with isolated microtia. By Gene Ontology/Kyoto Encyclopedia of Genes and Genomes pathway (GO/KEGG) analysis, we identified 27 differentially expressed genes enriched in pathways associated with microtia. In addition, we predicted 9 differentially expressed genes as potential cis-acting targets of 12 differentially expressed lncRNAs. Our findings by qRT-PCR demonstrate significantly elevated expression levels of ZFAS1 and DAB1-AS1, whereas ADIRF-AS1, HOTAIRM1, and EPB41L4A-AS1 exhibited significantly reduced expression levels in the auricular cartilage tissues of patients with isolated microtia. Conclusions: Our study sheds light on the potential involvement of lncRNAs in microtia and provides a basis for further investigation into their functional roles and underlying mechanisms.

Changes in the Transcriptome and Proteome of Cartilage in Microtia

ABSTRACT

Congenital microtia is a severe physiological defect and is among the most common craniofacial defects. It is characterized by severe auricle dysplasia, external auditory canal atresia or stenosis, and middle ear malformation, though inner ear development is mostly normal with some hearing occurring through bone conduction. Auricular reconstruction is the only treatment for congenital microtia. In this study, the authors integrated messenger ribonucleic acid and mass spectrometry data of cartilage obtained from the affected and unaffected sides of 16 unilateral microtia patients who had undergone ear reconstruction surgery. The authors next performed functional analyses to investigate differences in the proteome of the affected and unaffected ears to elicit molecular pathways involved in microtia pathogenesis. The authors collected 16 pairs samples. Proteomic and transcriptomic analyses identified 47 genes that were differentially expressed in affected and unaffected cartilage. Integrated pathway analysis implicated the involvement of genes related to cell adhesion, extracellular matrix organization, and cell migration in disease progression. Through the integration of gene and protein expression data in human primary chondrocytes, the authors identified molecular markers of microtia progression that were replicated across independent datasets and that have translational potential.

New novel non-MHC genes were identified for cervical cancer with an integrative analysis approach of transcriptome-wide association study

Although genome-wide association studies (GWAS) have successfully identified multiple genetic variants associated with cervical cancer, the functional role of those variants is not well understood. To bridge such gap, we integrated the largest cervical cancer GWAS (N = 9,347) with gene expression measured in six human tissues to perform a multi-tissue transcriptome-wide association study (TWAS). We identified a total of 20 associated genes in the European population, especially four novel non-MHC genes (i.e. WDR19, RP11-384K6.2, RP11-384K6.6 and ITSN1). Further, we attempted to validate our results in another independent cervical cancer GWAS from the East Asian population (N = 3,314) and re-discovered four genes including WDR19, HLA-DOB, MICB and OR2B8P. In our subsequent co-expression analysis, we discovered SLAMF7 and LTA were co-expressed in TCGA tumor samples and showed both WDR19 and ITSN1 were enriched in "plasma membrane". Using the protein-protein interaction analysis we observed strong interactions between the proteins produced by genes that are associated with cervical cancer. Overall, our study identified multiple candidate genes, especially four non-MHC genes, which may be causally associated with the risk of cervical cancer. However, further investigations with larger sample size are warranted to validate our findings in diverse populations.

MALAT1: A long non-coding RNA highly associated with human cancers

Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a well-known lncRNA associated with numerous diseases, particularly cancer, has received increased attention. The expression of MALAT1 was determined to be upregulated in numerous types of tumors and MALAT1 exhibited effects on tumor cell proliferation, migration, invasion and apoptosis. The abnormal expression of MALAT1 was identified in almost in every organ of the digestive system. MALAT1 performed an important role in the pathological alterations of organs that are associated with sex hormones and several reproductive system cancers. MALAT1 participates in molecular pathways. In the clinical application of MALAT1, MALAT1 was considered as a potential biomarker for the diagnosis and prediction of cancers, and may also serve as therapeutic target for treatment of specific tumors. This review summarizes the abnormal expression of MALAT1 in cancer, its significant effect on the primary features of cancer, as well as the underlying molecular mechanisms of MALAT1 in various cancers. According to studies on MALAT1, we introduce the upstream and downstream substances associated with the function of MALAT1. These reviewed studies promote the clinical application of MALAT1 in the aspect of diagnosis and treatment of different cancers, and may help point out new study directions for MALAT1.

Integrated analysis of long non‑coding RNA competing interactions revealed potential biomarkers in cervical cancer: Based on a public database

Cervical cancer (CC) is a common gynecological malignancy in women worldwide. Using an RNA sequencing profile from The Cancer Genome Atlas (TCGA) and the CC patient information, the aim of the present study was to identify potential long non‑coding RNA (lncRNA) biomarkers of CC using bioinformatics analysis and building a competing endogenous RNA (ceRNA) co‑expression network. Results indicated several CC‑specific lncRNAs, which were associated with CC clinical information and selected some of them for validation and evaluated their diagnostic values. Bioinformatics analysis identified 51 CC‑specific lncRNAs (fold‑change >2 and P<0.05), and 42 of these were included in ceRNA network consisting of lncRNA‑miRNA‑mRNA interactions. Further analyses revealed that differential expression levels of 19 lncRNAs were significantly associated with different clinical features (P<0.05). A total of 11 key lncRNAs in the ceRNA network for reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) analysis to detect their expression levels in 31 pairs of CC clinical samples. The results indicated that 7 lncRNAs were upregulated and 4 lncRNAs were downregulated in CC patients. The fold‑changes between the RT‑qPCR experiments and the TCGA bioinformatics analyses were the same. Furthermore, the area under the receiver operating characteristic (ROC) curve of four lncRNAs (EMX20S, MEG3, SYS1‑DBNDD2 and MIR9‑3HG) indicated that their combined use may have a significant diagnostic value in CC (P<0.05). To the best of our knowledge, the present study is the first to have identified CC‑specific lncRNAs to construct a ceRNA network and has also provided new insights for further investigation of a lncRNA‑associated ceRNA network in CC. In additon, the verification results suggested that the method of bioinformatics analysis and screening of lncRNAs was accurate and reliable. To conclude, the use of multiple lncRNAs may thus improve diagnostic efficacy in CC. In addition, these specific lncRNAs may serve as new candidate biomarkers for clinical diagnosis, classification and prognosis of CC.

Differential expression of long noncoding RNAs in congenital microtia

OBJECTIVE

To analyse lncRNA expression profiles in microtia using bioinformatics analysis.

METHODS

We examined lncRNA expression profiles in residual ear cartilage and normal ear cartilage from individual congenital microtia patients.

RESULTS

The gene chips used in this study included 30586 lncRNAs and 26109 mRNA probes. Intotal, 180 lncRNAs with differential expression weredetected in the residual ear cartilage compared with the normal cartilage, including 74 up-regulated and 106down-regulated lncRNAs. Signalling pathway analysis highlighted glyceride metabolism, osteoclast differentiation, andtumour growth. The results of qRT-PCR analysis were consistent with those of themicroarray.

CONCLUSION

Differential expression of lncRNAs occurs in microtia. These lncRNAs and related signalling pathways may play an important role in the occurrence and development ofmicrotia.

Chondrocytes from congenital microtia possess an inferior capacity for in vivo cartilage regeneration to healthy ear chondrocytes

The remnant auricular cartilage from microtia has become a valuable cell source for ear regeneration. It is important to clarify the issue of whether the genetically defective microtia chondrocytes could engineer cartilage tissue comparable to healthy ear chondrocytes. In the current study, the histology and cell yield of native microtia and normal ear cartilage were investigated, and the biological characteristics of derived chondrocytes examined, including proliferation, chondrogenic phenotype and cell migration. Furthermore, the in vivo cartilage-forming capacity of passaged microtia and normal auricular chondrocytes were systematically compared by seeding them onto polyglycolic acid/polylactic acid scaffold to generate tissue engineered cartilage in nude mice. Through histological examinations and quantitative analysis of glycosaminoglycan, Young's modulus, and the expression of cartilage-related genes, it was found that microtia chondrocytes had a slower dedifferentiation rate with the decreased expression of stemness-related genes, and weaker migration ability than normal ear chondrocytes, and the microtia chondrocytes-engineered cartilage was biochemically and biomechanically inferior to that constructed using normal ear chondrocytes. This study provides valuable information for the clinical application of the chondrocytes derived from congenital microtia to engineer cartilage. Copyright © 2016 John Wiley & Sons, Ltd.

Integrated analysis of long non-coding RNA‑associated ceRNA network reveals potential lncRNA biomarkers in human lung adenocarcinoma

Accumulating evidence has highlighted the important roles of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in tumor biology. However, the roles of cancer specific lncRNAs in lncRNA-related ceRNA network of lung adenocarcinoma (LUAD) are still unclear. In the present study, the 465 RNA sequencing profiles in LUAD patients were obtained from the cancer genome atlas (TCGA) database, which provides large sample RNA sequencing data free of charge, and 41 cancer specific lncRNAs, 25 miRNAs and 1053 mRNAs (fold change >2, p<0.05) were identified. Then, the lncRNA-miRNA-mRNA ceRNA network of LUAD was constructed with 29 key lncRNAs, 24 miRNAs and 72 mRNAs. Subsequently, we selected these 29 key lncRNAs to analyze their correlation with clinical features, and 21 of them were aberrantly expressed with tumor pathological stage, TNM staging system, lymph node metastasis and patient outcome assessment, respectively. Furthermore, there were 5 lncRNAs (BCRP3, LINC00472, CHIAP2, BMS1P20 and UNQ6494) positively correlated with overall survival (OS, log-rank p<0.05). Finally, 7 cancer specific lncRNAs were randomly selected to verify the expression in 53 newly diagnosed LUAD patients using qRT-PCR. The expression results between TCGA and qRT-PCR were 100% in agreement. The correlation between AFAP1-AS1 and LINC00472 and clinical features were also confirmed. Thus, our results showed the lncRNA expression profiles and we constructed an lncRNA-miRNA-mRNA ceRNA network in LUAD. The present study provides novel insight for better understanding of lncRNA-related ceRNA network in LUAD and facilitates the identification of potential biomarkers for diagnosis and prognosis.